In comments on this post, Tim and Ohioan both noted that the massive numbers of fruit flies breeding were enough to lead to macro-evolutionary changes over time. Even if the odds were billions-to-one against advantageous structural changes in genetic material, the fact that there are so many fruit flies producing so many offspring makes it conceivable.
Hooray for fruit flies!
How about elephants?
There aren't many of them and elephant cows produce a single calf every 5 years or so. Wouldn't evolution grind to a halt as the higher-order species produced so few offspring? If you need a billion hatchlings / calves / lambs to get a single new species with a new genetic structure instead of modification to existing genes, wouldn't it take practically forever to make those changes?
I've got a counter-argument to this line of thought, but I'm interested in what others have to say.
Aside: The original posts weren't really designed to question evolution, but were about Darwinian dogma being essentially religious. Still, it's a fun discussion and everyone's been quite pleasant, so let's see where else it goes.